#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
SEPT12	124404	broad.mit.edu	37	16	4834039	4834039	+	Silent	SNP	C	C	T			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr16:4834039C>T	ENST00000268231.8	-	5	668	c.405G>A	c.(403-405)gaG>gaA	p.E135E	SEPT12_ENST00000591861.1_5'Flank|SEPT12_ENST00000396693.5_Intron	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	135	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						GCTCGTATTGCTCGTTGATGT	0.627																																						ENST00000268231.8																			0				NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						c.(403-405)gaG>gaA		septin 12							185.0	162.0	170.0					16																	4834039		2197	4300	6497	SO:0001819	synonymous_variant	124404				cell cycle|cell division	cleavage furrow|midbody|perinuclear region of cytoplasm|septin complex|spindle|stress fiber	GDP binding|GTP binding|phosphatidylinositol binding|protein homodimerization activity	g.chr16:4834039C>T	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.405G>A	16.37:g.4834039C>T						SEPT12_ENST00000396693.5_Intron	p.E135E	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN			5	668	-			135					Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	c.405G>A	CCDS10522.1																																																																																				0.627	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605		32	75	0	0	0	1	0	32	75				
CAPNS2	84290	broad.mit.edu	37	16	55601279	55601279	+	Missense_Mutation	SNP	T	T	C	rs567078741		TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr16:55601279T>C	ENST00000457326.2	+	1	696	c.611T>C	c.(610-612)aTg>aCg	p.M204T	LPCAT2_ENST00000565056.1_Intron|LPCAT2_ENST00000262134.5_Intron	NM_032330.1	NP_115706.1	Q96L46	CPNS2_HUMAN	calpain, small subunit 2	204	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|large_intestine(1)|lung(3)|prostate(2)	7						GATGGAGATATGGATTTTAAC	0.478													T|||	1	0.000199681	0.0	0.0	5008	,	,		20408	0.001		0.0	False		,,,				2504	0.0					ENST00000457326.2																			0				central_nervous_system(1)|large_intestine(1)|lung(3)|prostate(2)	7						c.(610-612)aTg>aCg		calpain, small subunit 2							189.0	186.0	187.0					16																	55601279		1954	4158	6112	SO:0001583	missense	84290					cytoplasm|plasma membrane	calcium ion binding	g.chr16:55601279T>C	AY052551	CCDS54010.1	16q12.2	2013-01-10						"""EF-hand domain containing"""	16371	protein-coding gene	gene with protein product						11853546	Standard	NM_032330		Approved	MGC12536, MGC14804	uc002eid.1	Q96L46		ENST00000457326.2:c.611T>C	16.37:g.55601279T>C	ENSP00000400882:p.Met204Thr					LPCAT2_ENST00000565056.1_Intron|LPCAT2_ENST00000262134.5_Intron	p.M204T	NM_032330.1	NP_115706.1	Q96L46	CPNS2_HUMAN			1	696	+			204			EF-hand 3.		Q9BPV4	Missense_Mutation	SNP	ENST00000457326.2	37	c.611T>C	CCDS54010.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.298276	0.60195	.	.	ENSG00000256812	ENST00000457326	T	0.46819	0.86	5.98	5.98	0.97165	EF-hand-like domain (1);	.	.	.	.	T	0.63414	0.2509	M	0.78801	2.425	0.58432	D	0.999993	P	0.51537	0.946	P	0.52481	0.7	T	0.68693	-0.5341	9	0.87932	D	0	.	16.4781	0.84144	0.0:0.0:0.0:1.0	.	204	Q96L46	CPNS2_HUMAN	T	204	ENSP00000400882:M204T	ENSP00000400882:M204T	M	+	2	0	CAPNS2	54158780	1.000000	0.71417	0.996000	0.52242	0.275000	0.26752	7.698000	0.84413	2.288000	0.76882	0.528000	0.53228	ATG		0.478	CAPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396391.1	NM_032330		5	169	0	0	0	1	0	5	169				
BACH1	571	broad.mit.edu	37	21	30693752	30693752	+	Missense_Mutation	SNP	G	G	A	rs149732438	byFrequency	TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr21:30693752G>A	ENST00000399921.1	+	2	394	c.151G>A	c.(151-153)Gtg>Atg	p.V51M	BACH1_ENST00000286800.3_Missense_Mutation_p.V51M	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						TCACCGGTCCGTGCTGGCGGC	0.522																																						ENST00000399921.1																			0				breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						c.(151-153)Gtg>Atg		BTB and CNC homology 1, basic leucine zipper transcription factor 1		G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	121.0	100.0	107.0		151,151	3.5	0.6	21	dbSNP_134	107	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BACH1	NM_001186.2,NM_206866.1	21,21	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	51/737,51/737	30693752	2,13004	2203	4300	6503	SO:0001583	missense	571					nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr21:30693752G>A	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.151G>A	21.37:g.30693752G>A	ENSP00000382805:p.Val51Met					BACH1_ENST00000286800.3_Missense_Mutation_p.V51M	p.V51M	NM_206866.1	NP_996749.1	O14867	BACH1_HUMAN			2	394	+			51			BTB.		Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	37	c.151G>A	CCDS13585.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.205003	0.79127	2.27E-4	1.16E-4	ENSG00000156273	ENST00000286800;ENST00000399921;ENST00000451655;ENST00000447177;ENST00000435072	T;T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77;-0.77	5.33	3.5	0.40072	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.169650	0.40385	N	0.001113	D	0.83880	0.5350	M	0.92604	3.325	0.58432	D	0.999992	D	0.76494	0.999	P	0.52598	0.703	D	0.85822	0.1386	9	.	.	.	-11.384	10.7617	0.46268	0.0688:0.0:0.8007:0.1305	.	51	O14867	BACH1_HUMAN	M	51	ENSP00000286800:V51M;ENSP00000382805:V51M;ENSP00000400576:V51M;ENSP00000408605:V51M;ENSP00000392202:V51M	.	V	+	1	0	BACH1	29615623	1.000000	0.71417	0.603000	0.28903	0.830000	0.47004	5.152000	0.64882	0.719000	0.32188	0.557000	0.71058	GTG		0.522	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		4	57	0	0	0	1	0	4	57				
CSRNP1	64651	broad.mit.edu	37	3	39185421	39185421	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr3:39185421G>A	ENST00000273153.5	-	5	1072	c.895C>T	c.(895-897)Cgc>Tgc	p.R299C	CSRNP1_ENST00000514182.1_Missense_Mutation_p.R299C	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	299					apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						AACTGCAGGCGGGTGAGTGTG	0.607																																						ENST00000273153.5																			0				central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						c.(895-897)Cgc>Tgc		cysteine-serine-rich nuclear protein 1							40.0	39.0	39.0					3																	39185421		2203	4300	6503	SO:0001583	missense	64651				apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr3:39185421G>A	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"""AXIN1 up-regulated 1"""	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.895C>T	3.37:g.39185421G>A	ENSP00000273153:p.Arg299Cys					CSRNP1_ENST00000514182.1_Missense_Mutation_p.R299C	p.R299C	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN			5	1072	-			299					Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	37	c.895C>T	CCDS2682.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705170	0.68615	.	.	ENSG00000144655	ENST00000273153;ENST00000514182	T;T	0.15718	2.4;2.4	4.46	3.51	0.40186	.	0.266108	0.34435	N	0.003975	T	0.34774	0.0909	M	0.76838	2.35	0.58432	D	0.999997	D	0.76494	0.999	P	0.59288	0.855	T	0.14282	-1.0478	10	0.87932	D	0	-29.1159	10.2687	0.43470	0.0:0.0:0.6141:0.3859	.	299	Q96S65	CSRN1_HUMAN	C	299	ENSP00000273153:R299C;ENSP00000422532:R299C	ENSP00000273153:R299C	R	-	1	0	CSRNP1	39160425	0.996000	0.38824	1.000000	0.80357	0.981000	0.71138	0.923000	0.28757	2.466000	0.83321	0.549000	0.68633	CGC		0.607	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		3	26	0	0	0	1	0	3	26				
AMZ2P1	201283	broad.mit.edu	37	17	62968690	62968690	+	RNA	SNP	A	A	G			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr17:62968690A>G	ENST00000430983.1	-	0	1554					NR_026903.1				archaelysin family metallopeptidase 2 pseudogene 1																		AAAATTCCACAAGTCTCTTGG	0.373																																						ENST00000430983.1																			0																																																			0							g.chr17:62968690A>G	AK056627		17q24.1	2012-10-16	2010-04-08		ENSG00000214174	ENSG00000214174			26491	pseudogene	pseudogene							Standard	NR_026903		Approved	FLJ32065	uc002jfb.3		OTTHUMG00000132075		17.37:g.62968690A>G								NR_026903.1						0	1554	-									RNA	SNP	ENST00000430983.1	37																																																																																						0.373	AMZ2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255102.1	NM_153032		4	89	0	0	0	1	0	4	89				
IGHV3-49	28423	broad.mit.edu	37	14	107012975	107012975	+	RNA	SNP	A	A	G			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr14:107012975A>G	ENST00000390625.2	-	0	399									immunoglobulin heavy variable 3-49																		CTCGGTTTTCAGGCTGTTCAT	0.517																																						ENST00000390625.2																			0																				148.0	143.0	145.0					14																	107012975		1963	4149	6112			0							g.chr14:107012975A>G	M99676		14q32.33	2012-02-08			ENSG00000211965	ENSG00000211965		"""Immunoglobulins / IGH locus"""	5607	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000151967		14.37:g.107012975A>G														0	399	-									RNA	SNP	ENST00000390625.2	37																																																																																						0.517	IGHV3-49-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000324613.1	NG_001019		5	172	0	0	0	1	0	5	172				
CCT6B	10693	broad.mit.edu	37	17	33279009	33279009	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr17:33279009C>T	ENST00000314144.5	-	5	689	c.574G>A	c.(574-576)Gaa>Aaa	p.E192K	CCT6B_ENST00000436961.3_Missense_Mutation_p.E147K|CCT6B_ENST00000421975.3_Missense_Mutation_p.E192K	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	192					chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)	p.E192Q(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				TCCATTATTTCTACCATGAAG	0.318																																						ENST00000314144.5																			1	Substitution - Missense(1)	p.E192Q(1)	ovary(1)	NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20						c.(574-576)Gaa>Aaa		chaperonin containing TCP1, subunit 6B (zeta 2)							103.0	97.0	99.0					17																	33279009		2203	4300	6503	SO:0001583	missense	10693				chaperone-mediated protein complex assembly|protein folding|spermatogenesis	cytoplasm	ATP binding|protein transporter activity|unfolded protein binding	g.chr17:33279009C>T	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.574G>A	17.37:g.33279009C>T	ENSP00000327191:p.Glu192Lys					CCT6B_ENST00000436961.3_Missense_Mutation_p.E147K|CCT6B_ENST00000421975.3_Missense_Mutation_p.E192K	p.E192K	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN			5	689	-		Ovarian(249;0.17)	192					B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	c.574G>A	CCDS32617.1	.	.	.	.	.	.	.	.	.	.	C	19.63	3.863828	0.71949	.	.	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.77358	0.14;-1.09;-1.09	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	D	0.83358	0.5237	L	0.49513	1.565	0.80722	D	1	P;D;D	0.89917	0.944;1.0;1.0	D;D;D	0.91635	0.928;0.999;0.999	T	0.78588	-0.2146	10	0.17832	T	0.49	-21.0335	15.6109	0.76716	0.0:1.0:0.0:0.0	.	147;192;192	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	K	192;192;147	ENSP00000398044:E192K;ENSP00000327191:E192K;ENSP00000400917:E147K	ENSP00000327191:E192K	E	-	1	0	CCT6B	30303122	1.000000	0.71417	0.923000	0.36655	0.236000	0.25371	6.653000	0.74382	2.627000	0.88993	0.655000	0.94253	GAA		0.318	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584		4	32	0	0	0	1	0	4	32				
ANKRD30BP2	149992	broad.mit.edu	37	21	14414902	14414902	+	RNA	SNP	G	G	A	rs2821609		TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr21:14414902G>A	ENST00000507941.1	+	0	95									ankyrin repeat domain 30B pseudogene 2																		CCAGCTTGACGTCCTTGATGG	0.443																																						ENST00000507941.1																			0																																																			0							g.chr21:14414902G>A	AF427490		21q11.2	2010-06-14	2010-06-14	2010-06-14	ENSG00000224309	ENSG00000224309			16620	pseudogene	pseudogene	"""cancer/testis antigen 85"""		"""chromosome 21 open reading frame 99"""	C21orf99		12036297, 17114284	Standard	NR_026916		Approved	CT85, CTSP-1	uc002yja.4		OTTHUMG00000074164		21.37:g.14414902G>A														0	95	+									RNA	SNP	ENST00000507941.1	37																																																																																						0.443	ANKRD30BP2-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000372094.1	NR_026916		5	28	0	0	0	1	0	5	28				
NMD3	51068	broad.mit.edu	37	3	160967245	160967245	+	Missense_Mutation	SNP	T	T	G			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr3:160967245T>G	ENST00000460469.1	+	13	1662	c.1207T>G	c.(1207-1209)Tta>Gta	p.L403V	NMD3_ENST00000472947.1_Missense_Mutation_p.L403V|NMD3_ENST00000351193.2_Missense_Mutation_p.L403V			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	403					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			CTTGCAGGTATTAATCAAGAA	0.363																																						ENST00000460469.1																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25						c.(1207-1209)Tta>Gta		NMD3 ribosome export adaptor							58.0	58.0	58.0					3																	160967245		2203	4300	6503	SO:0001583	missense	51068				protein transport	cytoplasm|nucleolus|nucleoplasm		g.chr3:160967245T>G	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"""NMD3 homolog (S. cerevisiae)"""			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.1207T>G	3.37:g.160967245T>G	ENSP00000419004:p.Leu403Val					NMD3_ENST00000472947.1_Missense_Mutation_p.L403V|NMD3_ENST00000351193.2_Missense_Mutation_p.L403V	p.L403V			Q96D46	NMD3_HUMAN	Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)		13	1662	+			403					D3DNM7|Q9Y2Z6	Missense_Mutation	SNP	ENST00000460469.1	37	c.1207T>G	CCDS3194.1	.	.	.	.	.	.	.	.	.	.	T	12.56	1.975475	0.34848	.	.	ENSG00000169251	ENST00000351193;ENST00000472947;ENST00000460469;ENST00000540137	T;T;T	0.26067	1.76;1.76;1.76	4.84	1.1	0.20463	.	0.078628	0.53938	D	0.000056	T	0.51278	0.1665	M	0.93375	3.41	0.44227	D	0.997061	D;D;P	0.63046	0.977;0.992;0.908	P;P;B	0.58970	0.762;0.849;0.256	T	0.57579	-0.7787	10	0.87932	D	0	-16.2214	9.1722	0.37089	0.0:0.3066:0.0:0.6934	.	403;403;403	B3KT11;C9JA08;Q96D46	.;.;NMD3_HUMAN	V	403;403;403;283	ENSP00000307525:L403V;ENSP00000417559:L403V;ENSP00000419004:L403V	ENSP00000307525:L403V	L	+	1	2	NMD3	162449939	0.775000	0.28604	0.325000	0.25375	0.854000	0.48673	1.182000	0.32029	0.091000	0.17302	0.482000	0.46254	TTA		0.363	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938		3	10	0	0	0	1	0	3	10				
CILP	8483	broad.mit.edu	37	15	65490925	65490925	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr15:65490925C>T	ENST00000261883.4	-	9	1865	c.1699G>A	c.(1699-1701)Gaa>Aaa	p.E567K		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	567					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						ATCTTGATTTCATGGAACACG	0.517																																						ENST00000261883.4																			0				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						c.(1699-1701)Gaa>Aaa		cartilage intermediate layer protein, nucleotide pyrophosphohydrolase							73.0	66.0	68.0					15																	65490925		2202	4299	6501	SO:0001583	missense	8483				negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix		g.chr15:65490925C>T	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.1699G>A	15.37:g.65490925C>T	ENSP00000261883:p.Glu567Lys						p.E567K	NM_003613.3	NP_003604.3	O75339	CILP1_HUMAN			9	1865	-			567					B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	c.1699G>A	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605809	0.66445	.	.	ENSG00000138615	ENST00000261883	T	0.49720	0.77	5.63	5.63	0.86233	.	0.045955	0.85682	D	0.000000	T	0.58793	0.2147	M	0.68952	2.095	0.80722	D	1	D	0.53885	0.963	P	0.50082	0.63	T	0.60172	-0.7315	10	0.49607	T	0.09	-10.3916	18.6978	0.91607	0.0:1.0:0.0:0.0	.	567	O75339	CILP1_HUMAN	K	567	ENSP00000261883:E567K	ENSP00000261883:E567K	E	-	1	0	CILP	63277978	1.000000	0.71417	0.989000	0.46669	0.562000	0.35680	7.814000	0.86154	2.652000	0.90054	0.655000	0.94253	GAA		0.517	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		6	58	0	0	0	1	0	6	58				
OR2L3	391192	broad.mit.edu	37	1	248224912	248224912	+	Missense_Mutation	SNP	G	G	T			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr1:248224912G>T	ENST00000359959.3	+	1	929	c.929G>T	c.(928-930)gGg>gTg	p.G310V	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	310						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			ATCTGCTCTGGGAAAATGTAG	0.438																																						ENST00000359959.3																			0				cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41						c.(928-930)gGg>gTg		olfactory receptor, family 2, subfamily L, member 3							38.0	39.0	38.0					1																	248224912		2203	4300	6503	SO:0001583	missense	391192				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248224912G>T	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.929G>T	1.37:g.248224912G>T	ENSP00000353044:p.Gly310Val					OR2L13_ENST00000366478.2_Intron	p.G310V	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0278)		1	929	+	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		310					B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	c.929G>T	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	G	0.021	-1.427257	0.01117	.	.	ENSG00000198128	ENST00000359959	T	0.10477	2.87	1.43	-2.86	0.05717	.	.	.	.	.	T	0.04452	0.0122	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41431	-0.9509	9	0.25751	T	0.34	.	1.3116	0.02099	0.1592:0.127:0.3444:0.3694	.	310	Q8NG85	OR2L3_HUMAN	V	310	ENSP00000353044:G310V	ENSP00000353044:G310V	G	+	2	0	OR2L3	246291535	0.011000	0.17503	0.000000	0.03702	0.038000	0.13279	-0.747000	0.04823	-1.031000	0.03308	-1.998000	0.00445	GGG		0.438	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		3	34	1	0	0.004672	1	0.00489448	3	34				
CCT6B	10693	broad.mit.edu	37	17	33288338	33288338	+	Silent	SNP	G	G	A			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr17:33288338G>A	ENST00000314144.5	-	1	190	c.75C>T	c.(73-75)tgC>tgT	p.C25C	CCT6B_ENST00000436961.3_Silent_p.C25C|ZNF830_ENST00000361952.3_5'Flank|CCT6B_ENST00000421975.3_Silent_p.C25C	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	25				AALAVNICAARGL -> QLWLSIYAPPRV (in Ref. 1; BAA11347). {ECO:0000305}.	chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				CTCGGGCGGCGCATATATTGA	0.592																																						ENST00000314144.5																			0				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20						c.(73-75)tgC>tgT		chaperonin containing TCP1, subunit 6B (zeta 2)							33.0	36.0	35.0					17																	33288338		2203	4300	6503	SO:0001819	synonymous_variant	10693				chaperone-mediated protein complex assembly|protein folding|spermatogenesis	cytoplasm	ATP binding|protein transporter activity|unfolded protein binding	g.chr17:33288338G>A	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.75C>T	17.37:g.33288338G>A						CCT6B_ENST00000436961.3_Silent_p.C25C|CCT6B_ENST00000421975.3_Silent_p.C25C	p.C25C	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN			1	190	-		Ovarian(249;0.17)	25	AALAVNICAARGL -> QLWLSIYAPPRV (in Ref. 1; BAA11347).				B4DX20|B4DYB0|Q8TC34	Silent	SNP	ENST00000314144.5	37	c.75C>T	CCDS32617.1																																																																																				0.592	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584		3	35	0	0	0	1	0	3	35				
SACS	26278	broad.mit.edu	37	13	23913960	23913960	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr13:23913960C>T	ENST00000382292.3	-	9	4328	c.4055G>A	c.(4054-4056)aGc>aAc	p.S1352N	SACS_ENST00000382298.3_Missense_Mutation_p.S1352N|SACS_ENST00000402364.1_Missense_Mutation_p.S602N			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1352					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ATTTTGTTTGCTTTCTTGTTC	0.368																																						ENST00000382298.3																			0				NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189						c.(4054-4056)aGc>aAc		spastic ataxia of Charlevoix-Saguenay (sacsin)							131.0	118.0	123.0					13																	23913960		2203	4300	6503	SO:0001583	missense	26278				cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding	g.chr13:23913960C>T	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.4055G>A	13.37:g.23913960C>T	ENSP00000371729:p.Ser1352Asn					SACS_ENST00000402364.1_Missense_Mutation_p.S602N|SACS_ENST00000382292.3_Missense_Mutation_p.S1352N	p.S1352N	NM_014363.4	NP_055178.3	Q9NZJ4	SACS_HUMAN		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)	10	4643	-		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)	1352					O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	c.4055G>A	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833562	0.50951	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.93859	-3.3;-3.3;-3.3	6.06	6.06	0.98353	.	0.039506	0.85682	D	0.000000	D	0.92322	0.7564	L	0.34521	1.04	0.40981	D	0.98477	D	0.54601	0.967	P	0.53102	0.718	D	0.91968	0.5584	10	0.46703	T	0.11	.	13.774	0.63041	0.0:0.9304:0.0:0.0696	.	1352	Q9NZJ4	SACS_HUMAN	N	1352;602;1352	ENSP00000371729:S1352N;ENSP00000385844:S602N;ENSP00000371735:S1352N	ENSP00000371729:S1352N	S	-	2	0	SACS	22811960	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.696000	0.61774	2.879000	0.98667	0.650000	0.86243	AGC		0.368	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		5	44	0	0	0	1	0	5	44				
IRS2	8660	broad.mit.edu	37	13	110436139	110436139	+	Missense_Mutation	SNP	C	C	A			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr13:110436139C>A	ENST00000375856.3	-	1	2776	c.2262G>T	c.(2260-2262)gaG>gaT	p.E754D		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	754					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			CATCTGCATGCTCCATGGACA	0.687																																					Melanoma(100;613 2409 40847)	ENST00000375856.3																			0				kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19						c.(2260-2262)gaG>gaT		insulin receptor substrate 2							25.0	15.0	18.0					13																	110436139		2092	4118	6210	SO:0001583	missense	8660				fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus	cytosol|plasma membrane	insulin receptor binding|signal transducer activity	g.chr13:110436139C>A	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2262G>T	13.37:g.110436139C>A	ENSP00000365016:p.Glu754Asp						p.E754D	NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)		1	2776	-	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	754					Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	37	c.2262G>T	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	C	5.850	0.340944	0.11069	.	.	ENSG00000185950	ENST00000375856	T	0.19250	2.16	4.06	1.29	0.21616	.	0.143697	0.46442	D	0.000285	T	0.15912	0.0383	L	0.52905	1.665	0.32297	N	0.565467	B	0.24963	0.115	B	0.22386	0.039	T	0.08289	-1.0729	10	0.34782	T	0.22	-17.7654	4.5353	0.12026	0.1515:0.5936:0.0:0.2549	.	754	Q9Y4H2	IRS2_HUMAN	D	754	ENSP00000365016:E754D	ENSP00000365016:E754D	E	-	3	2	IRS2	109234140	0.895000	0.30542	0.465000	0.27155	0.014000	0.08584	-0.036000	0.12185	0.385000	0.24970	-0.275000	0.10095	GAG		0.687	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749		3	5	1	0	0.115264	1	0.115264	3	5				
LARP7	51574	broad.mit.edu	37	4	113565889	113565889	+	Missense_Mutation	SNP	G	G	A	rs570445594	byFrequency	TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr4:113565889G>A	ENST00000344442.5	+	2	342	c.64G>A	c.(64-66)Gaa>Aaa	p.E22K	LARP7_ENST00000324052.6_Missense_Mutation_p.E22K|LARP7_ENST00000509061.1_Missense_Mutation_p.E29K|MIR302B_ENST00000505215.1_RNA|MIR302B_ENST00000509938.1_RNA|MIR302B_ENST00000510655.1_RNA	NM_016648.3	NP_057732.2	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	22					RNA processing (GO:0006396)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		AAAGAAAAAAGAAGTTGAAAA	0.353																																						ENST00000509061.1																			0				endometrium(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	17						c.(85-87)Gaa>Aaa		La ribonucleoprotein domain family, member 7							71.0	68.0	69.0					4																	113565889		1814	4071	5885	SO:0001583	missense	51574				RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding	g.chr4:113565889G>A	AF068284	CCDS3701.2, CCDS58924.1	4q25	2013-02-12			ENSG00000174720	ENSG00000174720		"""La ribonucleoprotein domain containing"", ""RNA binding motif (RRM) containing"""	24912	protein-coding gene	gene with protein product	"""P-TEFb-interaction protein for 7SK stability"""	612026				18191186, 18249148, 18281698, 22865833, 22488152	Standard	NM_016648		Approved	HDCMA18P, PIP7S, DKFZP564K112	uc003ibb.4	Q4G0J3	OTTHUMG00000132909	ENST00000344442.5:c.64G>A	4.37:g.113565889G>A	ENSP00000344950:p.Glu22Lys					LARP7_ENST00000344442.5_Missense_Mutation_p.E22K|LARP7_ENST00000324052.6_Missense_Mutation_p.E22K	p.E29K	NM_001267039.1	NP_001253968.1	Q4G0J3	LARP7_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000603)	4	388	+		Ovarian(17;0.0443)|Hepatocellular(203;0.217)	22			HTH La-type RNA-binding.		B2ZHN6|Q3B7A9|Q9P1S7|Q9Y3Z8	Missense_Mutation	SNP	ENST00000344442.5	37	c.85G>A	CCDS3701.2	.	.	.	.	.	.	.	.	.	.	G	19.54	3.846683	0.71603	.	.	ENSG00000174720	ENST00000344442;ENST00000509061;ENST00000508577;ENST00000505034;ENST00000324052;ENST00000507443	T;T;T;T;T;T	0.45276	2.16;2.16;0.9;2.14;2.16;0.92	5.02	5.02	0.67125	.	0.373600	0.32386	N	0.006174	T	0.43986	0.1272	M	0.65975	2.015	0.48830	D	0.999718	B;B	0.26635	0.155;0.155	B;B	0.24155	0.051;0.051	T	0.35748	-0.9776	10	0.23891	T	0.37	-9.5731	18.386	0.90466	0.0:0.0:1.0:0.0	.	22;22	D6RFF0;Q4G0J3	.;LARP7_HUMAN	K	22;29;22;22;22;22	ENSP00000344950:E22K;ENSP00000422626:E29K;ENSP00000426646:E22K;ENSP00000421541:E22K;ENSP00000314311:E22K;ENSP00000421963:E22K	ENSP00000314311:E22K	E	+	1	0	LARP7	113785338	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	9.350000	0.97070	2.303000	0.77524	0.644000	0.83932	GAA		0.353	LARP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256417.2	NM_016648		13	38	0	0	0	1	0	13	38				
RARRES2	5919	broad.mit.edu	37	7	150037252	150037252	+	Silent	SNP	C	C	T			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr7:150037252C>T	ENST00000466675.1	-	2	1249	c.216G>A	c.(214-216)ctG>ctA	p.L72L	RARRES2_ENST00000482669.1_Silent_p.L72L|RP4-584D14.7_ENST00000563946.1_RNA|RARRES2_ENST00000223271.3_Silent_p.L72L			Q99969	RARR2_HUMAN	retinoic acid receptor responder (tazarotene induced) 2	72					brown fat cell differentiation (GO:0050873)|chemotaxis (GO:0006935)|embryonic digestive tract development (GO:0048566)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|positive regulation of chemotaxis (GO:0050921)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of protein phosphorylation (GO:0001934)|regulation of lipid catabolic process (GO:0050994)|retinoid metabolic process (GO:0001523)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			TTGTCTGCTGCAGCTTAAATT	0.587																																						ENST00000466675.1																			0				endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)|skin(1)	5						c.(214-216)ctG>ctA		retinoic acid receptor responder (tazarotene induced) 2							271.0	286.0	281.0					7																	150037252		2203	4300	6503	SO:0001819	synonymous_variant	0				embryonic digestive tract development|in utero embryonic development|positive regulation of macrophage chemotaxis|retinoid metabolic process	extracellular matrix	receptor binding	g.chr7:150037252C>T	U77594	CCDS5902.1	7q36.1	2013-02-25			ENSG00000106538	ENSG00000106538		"""Endogenous ligands"""	9868	protein-coding gene	gene with protein product	"""chemerin"""	601973				9270552, 17767914	Standard	NM_002889		Approved	TIG2, HP10433	uc003wha.3	Q99969	OTTHUMG00000158325	ENST00000466675.1:c.216G>A	7.37:g.150037252C>T						RARRES2_ENST00000223271.3_Silent_p.L72L|RARRES2_ENST00000482669.1_Silent_p.L72L	p.L72L			Q99969	RARR2_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.011)		2	1249	-			72					Q7LE02	Silent	SNP	ENST00000466675.1	37	c.216G>A	CCDS5902.1																																																																																				0.587	RARRES2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350693.1			19	427	0	0	0	1	0	19	427				
DDX46	9879	broad.mit.edu	37	5	134153187	134153187	+	Splice_Site	SNP	A	A	G			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr5:134153187A>G	ENST00000354283.4	+	20	2747	c.2612A>G	c.(2611-2613)gAt>gGt	p.D871G	DDX46_ENST00000452510.2_Splice_Site_p.D872G			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	871					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TAACTACAGGATGTGATGCAG	0.423																																					Colon(13;391 453 4901 21675 24897)	ENST00000452510.2																			0				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						c.e20-1		DEAD (Asp-Glu-Ala-Asp) box polypeptide 46							50.0	49.0	49.0					5																	134153187		2203	4300	6503	SO:0001630	splice_region_variant	9879				mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding	g.chr5:134153187A>G		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"""DEAD-boxes"""	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.2611-1A>G	5.37:g.134153187A>G						DDX46_ENST00000354283.4_Splice_Site_p.D871_splice	p.D872_splice	NM_014829.2	NP_055644.2	Q7L014	DDX46_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)		20	2773	+			871					O94894|Q96EI0|Q9Y658	Splice_Site	SNP	ENST00000354283.4	37	c.2613_splice	CCDS34240.1	.	.	.	.	.	.	.	.	.	.	A	14.35	2.510157	0.44660	.	.	ENSG00000145833	ENST00000452510;ENST00000354283	T;T	0.25749	1.78;1.79	5.8	5.8	0.92144	.	0.091642	0.85682	D	0.000000	T	0.23249	0.0562	L	0.39898	1.24	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.05068	-1.0908	10	0.18710	T	0.47	-27.3238	16.1596	0.81693	1.0:0.0:0.0:0.0	.	871	Q7L014	DDX46_HUMAN	G	872;871	ENSP00000416534:D872G;ENSP00000346236:D871G	ENSP00000346236:D871G	D	+	2	0	DDX46	134181086	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.273000	0.95719	2.216000	0.71823	0.533000	0.62120	GAT		0.423	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829	Missense_Mutation	10	17	0	0	0	1	0	10	17				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		20	43	0	0	0	1	0	20	43				
PDSS1	23590	broad.mit.edu	37	10	26994255	26994255	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr10:26994255G>A	ENST00000376215.5	+	4	321	c.268G>A	c.(268-270)Gaa>Aaa	p.E90K	PDSS1_ENST00000376203.5_Missense_Mutation_p.E90K	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	90					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						ACACAGTGGTGAAAAATACAC	0.363																																						ENST00000376215.5																			0				autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						c.(268-270)Gaa>Aaa		prenyl (decaprenyl) diphosphate synthase, subunit 1							80.0	73.0	75.0					10																	26994255		2203	4300	6503	SO:0001583	missense	23590				isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	metal ion binding|protein heterodimerization activity	g.chr10:26994255G>A	AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"""coenzyme Q1 homolog (yeast)"""	607429	"""trans-prenyltransferase"""	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.268G>A	10.37:g.26994255G>A	ENSP00000365388:p.Glu90Lys					PDSS1_ENST00000376203.5_Missense_Mutation_p.E90K	p.E90K	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN			4	321	+			90					Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Missense_Mutation	SNP	ENST00000376215.5	37	c.268G>A	CCDS31168.1	.	.	.	.	.	.	.	.	.	.	G	33	5.222598	0.95139	.	.	ENSG00000148459	ENST00000376215;ENST00000376203;ENST00000396343	D	0.83250	-1.7	5.33	5.33	0.75918	Terpenoid synthase (1);	0.173333	0.49916	D	0.000121	D	0.88332	0.6408	L	0.59436	1.845	0.49582	D	0.999801	D;P	0.62365	0.991;0.572	P;B	0.59424	0.857;0.052	D	0.89211	0.3564	10	0.66056	D	0.02	-13.5851	17.7749	0.88504	0.0:0.0:1.0:0.0	.	90;90	Q5T2R2-2;Q5T2R2	.;DPS1_HUMAN	K	90;90;51	ENSP00000365388:E90K	ENSP00000365376:E90K	E	+	1	0	PDSS1	27034261	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	4.668000	0.61568	2.470000	0.83445	0.650000	0.86243	GAA		0.363	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1			5	25	0	0	0	1	0	5	25				
PRPF4B	8899	broad.mit.edu	37	6	4032325	4032325	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr6:4032325A>G	ENST00000337659.6	+	2	674	c.574A>G	c.(574-576)Act>Gct	p.T192A	PRPF4B_ENST00000538861.1_Missense_Mutation_p.T178A	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	192	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				CAAAGAACGGACTAGACATAG	0.353																																						ENST00000337659.6																			0				breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22						c.(574-576)Act>Gct		pre-mRNA processing factor 4B							110.0	124.0	119.0					6																	4032325		2202	4300	6502	SO:0001583	missense	8899					catalytic step 2 spliceosome	ATP binding|protein binding|protein serine/threonine kinase activity	g.chr6:4032325A>G	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"""PRP4 pre-mRNA processing factor 4 homolog B (yeast)"""			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.574A>G	6.37:g.4032325A>G	ENSP00000337194:p.Thr192Ala					PRPF4B_ENST00000538861.1_Missense_Mutation_p.T178A	p.T192A	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN			2	674	+	Ovarian(93;0.0925)	all_hematologic(90;0.0895)	192			Arg/Lys-rich (basic).		A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	c.574A>G	CCDS4488.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.273433	0.23221	.	.	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.66995	-0.24;-0.19	5.44	4.29	0.51040	.	0.152620	0.45867	N	0.000333	T	0.18383	0.0441	N	0.08118	0	0.33973	D	0.647061	B	0.02656	0.0	B	0.04013	0.001	T	0.07520	-1.0768	10	0.06891	T	0.86	.	8.3274	0.32165	0.8489:0.0:0.1511:0.0	.	192	Q13523	PRP4B_HUMAN	A	192;178	ENSP00000337194:T192A;ENSP00000439331:T178A	ENSP00000337194:T192A	T	+	1	0	PRPF4B	3977324	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.850000	0.62889	0.912000	0.36772	0.379000	0.24179	ACT		0.353	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			6	127	0	0	0	1	0	6	127				
NIFK-AS1	254128	broad.mit.edu	37	2	122466739	122466739	+	RNA	DEL	G	G	-	rs201278872|rs6733674|rs201879622	byFrequency	TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr2:122466739delG	ENST00000419902.1	+	0	637					NR_037857.1																						tttttttgttgtttttttttt	0.458																																						ENST00000419902.1																			0																																																			0							g.chr2:122466739delG																													2.37:g.122466739delG								NR_037857.1						0	637	+									RNA	DEL	ENST00000419902.1	37																																																																																						0.458	AC018737.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000330755.2			4	5						4	5	---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130394186	130394186	+	Frame_Shift_Del	DEL	C	C	-			TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr3:130394186delC	ENST00000358511.6	+	36	6768	c.6737delC	c.(6736-6738)tccfs	p.S2246fs	COL6A6_ENST00000453409.2_Frame_Shift_Del_p.S2246fs	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	2246	Nonhelical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						AGAAGCACCTCCCATACCTTT	0.348																																						ENST00000358511.6																			0				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						c.(6736-6738)tcfs		collagen, type VI, alpha 6							50.0	46.0	47.0					3																	130394186		1872	4106	5978	SO:0001589	frameshift_variant	131873				axon guidance|cell adhesion	collagen		g.chr3:130394186delC	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.6737delC	3.37:g.130394186delC	ENSP00000351310:p.Ser2246fs					COL6A6_ENST00000453409.2_Frame_Shift_Del_p.S2246fs	p.S2246fs	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN			36	6768	+			2246			Nonhelical region.		A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Frame_Shift_Del	DEL	ENST00000358511.6	37	c.6737delC	CCDS46911.1																																																																																				0.348	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		2	4						2	4	---	---	---	---
CCT6P1	643253	broad.mit.edu	37	7	65226819	65226819	+	RNA	DEL	A	A	-	rs530400395	byFrequency	TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr7:65226819delA	ENST00000442266.1	+	0	1167				SNORA15_ENST00000384058.1_RNA					chaperonin containing TCP1, subunit 6 (zeta) pseudogene 1																		AATGGGGACCAAAAAAAAAAT	0.353													|||unknown(NO_COVERAGE)	16	0.00319489	0.0068	0.0	5008	,	,		14661	0.005		0.0	False		,,,				2504	0.002					ENST00000442266.1																			0																																																			0							g.chr7:65226819delA	BC052238, BC073761		7q11.21	2010-06-29	2008-09-22	2008-09-22	ENSG00000228409	ENSG00000228409			33094	pseudogene	pseudogene			"""chaperonin containing TCP1, subunit 6A (zeta 1) pseudogene 1"""	CCT6AP1			Standard	NR_003110		Approved		uc003tug.3		OTTHUMG00000156733		7.37:g.65226819delA														0	1167	+									RNA	DEL	ENST00000442266.1	37																																																																																						0.353	CCT6P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345507.1	NR_003110		2	4						2	4	---	---	---	---
NUTM2F	54754	broad.mit.edu	37	9	97080945	97080947	+	In_Frame_Del	DEL	AGA	AGA	-	rs150455117|rs112857574	byFrequency	TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr9:97080945_97080947delAGA	ENST00000253262.4	-	7	2091_2093	c.2071_2073delTCT	c.(2071-2073)tctdel	p.S691del	NUTM2F_ENST00000341207.4_In_Frame_Del_p.S676del|NUTM2F_ENST00000335456.7_Intron	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	691				Missing (in Ref. 2; AAI30391 and 3; CAB61394). {ECO:0000305}.				p.S557delS(1)									TGCTGGCAGGAGAAGGTGATGGG	0.611														3777	0.754193	0.6051	0.8084	5008	,	,		15297	0.8869		0.7227	False		,,,				2504	0.8129					ENST00000253262.4																			1	Deletion - In frame(1)	p.S557delS(1)	central_nervous_system(1)								c.(2071-2073)del		NUT family member 2F				2288,1260		619,1050,105						-3.0	0.0		dbSNP_134	20	5646,2060		2048,1550,255	no	coding	FAM22F	NM_017561.1		2667,2600,360	A1A1,A1R,RR		26.7324,35.513,29.5006				7934,3320				SO:0001651	inframe_deletion	54754							g.chr9:97080945_97080947delAGA		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.2071_2073delTCT	9.37:g.97080945_97080947delAGA	ENSP00000253262:p.Ser691del					NUTM2F_ENST00000335456.7_Intron|NUTM2F_ENST00000341207.4_In_Frame_Del_p.S676del	p.S691del	NM_017561.1	NP_060031.1					7	2091_2093	-								B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	In_Frame_Del	DEL	ENST00000253262.4	37	c.2071_2073delTCT	CCDS47994.1																																																																																				0.611	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561		4	2						4	2	---	---	---	---
EMG1	10436	broad.mit.edu	37	12	7080210	7080211	+	Splice_Site	INS	-	-	G	rs60117710|rs374779752|rs200041551		TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr12:7080210_7080211insG	ENST00000261406.6	+	2	266		c.e2-1		PHB2_ENST00000546111.1_5'Flank|EMG1_ENST00000546220.1_3'UTR|PHB2_ENST00000544134.1_5'Flank|PHB2_ENST00000440277.1_5'Flank|PHB2_ENST00000535923.1_5'Flank|PHB2_ENST00000399433.2_5'Flank|PHB2_ENST00000542912.1_5'Flank	NM_006331.7	NP_006322.4			EMG1 N1-specific pseudouridine methyltransferase																		CGGAGGCCGTAGTTTATTGTGG	0.569													GG|G|GG|deletion	5008	1.0	1.0	1.0	5008	,	,		18008	1.0		1.0	False		,,,				2504	1.0					ENST00000546220.1																			0													EMG1 N1-specific pseudouridine methyltransferase				3732,16		1865,2,7						3.0	1.0		dbSNP_129	28	7880,30		3934,12,9	no	frameshift	EMG1	NM_006331.7		5799,14,16	A1A1,A1R,RR		0.3793,0.4269,0.3946				11612,46				SO:0001630	splice_region_variant	10436				ribosomal small subunit biogenesis	cytoplasm|nucleolus	rRNA (pseudouridine) methyltransferase activity|rRNA binding	g.chr12:7080210_7080211insG	U72514	CCDS73430.1	12p13	2013-05-22	2013-05-22			ENSG00000126749			16912	protein-coding gene	gene with protein product		611531	"""EMG1 nucleolar protein homolog (S. cerevisiae)"""			9074930, 11935223, 19463982	Standard	NM_006331		Approved	C2F, NEP1, Grcc2f	uc001qsh.4	Q92979		ENST00000261406.6:c.124-1->G	12.37:g.7080211_7080211dupG						U47924.19_ENST00000564245.1_RNA|U47924.28_ENST00000261406.6_lincRNA				Q92979	NEP1_HUMAN			0	155_156	+									RNA	INS	ENST00000261406.6	37																																																																																						0.569	EMG1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006331	Intron	4	9						4	9	---	---	---	---
NLRC3	197358	broad.mit.edu	37	16	3594163	3594163	+	RNA	DEL	A	A	-	rs60164526		TCGA-EM-A3SU-01A-11D-A22Z-08	TCGA-EM-A3SU-10A-01D-A22Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	598f5833-ab0a-4167-9c12-80573a106ea8	1ef6114a-a3ca-4992-9510-4209bfd07727	g.chr16:3594163delA	ENST00000301749.7	-	0	3261				NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|LA16c-390H2.4_ENST00000573820.1_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						tgtctcgaggaaaaaaaaaaa	0.488																																						ENST00000301749.7																			0				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34								NLR family, CARD domain containing 3																																						197358				I-kappaB kinase/NF-kappaB cascade|negative regulation of NF-kappaB transcription factor activity|T cell activation	cytoplasm	ATP binding	g.chr16:3594163delA	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3594163delA						NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA		NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN			0	3261	-								Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	RNA	DEL	ENST00000301749.7	37																																																																																						0.488	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		2	4						2	4	---	---	---	---
